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PDBsum entry 1sil

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Hydrolase(o-glycosyl) PDB id
1sil
Jmol
Contents
Protein chain
381 a.a.
Ligands
DAN
Waters ×140
Superseded by: 2sil
PDB id:
1sil
Name: Hydrolase(o-glycosyl)
Structure: Sialidase complex with 2-deoxy-2,3- dehydro-n-acetyl-neuraminic acid (dana)
Source: (Salmonella typhimurium, strain lt2)
Authors: S.J.Crennell,E.F.Garman,W.G.Laver,E.R.Vimr,G.L.Taylor
Key ref: S.J.Crennell et al. (1993). Crystal structure of a bacterial sialidase (from Salmonella typhimurium LT2) shows the same fold as an influenza virus neuraminidase. Proc Natl Acad Sci U S A, 90, 9852-9856. PubMed id: 8234325 DOI: 10.1073/pnas.90.21.9852
Date:
24-May-93     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 381 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1073/pnas.90.21.9852 Proc Natl Acad Sci U S A 90:9852-9856 (1993)
PubMed id: 8234325  
 
 
Crystal structure of a bacterial sialidase (from Salmonella typhimurium LT2) shows the same fold as an influenza virus neuraminidase.
S.J.Crennell, E.F.Garman, W.G.Laver, E.R.Vimr, G.L.Taylor.
 
  ABSTRACT  
 
Sialidases (EC 3.2.1.18 or neuraminidases) remove sialic acid from sialoglycoconjugates, are widely distributed in nature, and have been implicated in the pathogenesis of many diseases. The three-dimensional structure of influenza virus sialidase is known, and we now report the three-dimensional structure of a bacterial sialidase, from Salmonella typhimurium LT2, at 2.0-A resolution and the structure of its complex with the inhibitor 2-deoxy-2,3-dehydro-N-acetylneuraminic acid at 2.2-A resolution. The viral enzyme is a tetramer; the bacterial enzyme, a monomer. Although the monomers are of similar size (approximately 380 residues), the sequence similarity is low (approximately 15%). The viral enzyme contains at least eight disulfide bridges, conserved in all strains, and binds Ca2+, which enhances activity; the bacterial enzyme contains one disulfide and does not bind Ca2+. Comparison of the two structures shows a remarkable similarity both in the general fold and in the spatial arrangement of the catalytic residues. However, an rms fit of 3.1 A between 264 C alpha atoms of the S. typhimurium enzyme and those from an influenza A virus reflects some major differences in the fold. In common with the viral enzyme, the bacterial enzyme active site consists of an arginine triad, a hydrophobic pocket, and a key tyrosine and glutamic acid, but differences in the interactions with the O4 and glycerol groups of the inhibitor reflect differing kinetics and substrate preferences of the two enzymes. The repeating "Asp-box" motifs observed among the nonviral sialidase sequences occur at topologically equivalent positions on the outside of the structure. Implications of the structure for the catalytic mechanism, evolution, and secretion of the enzyme are discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20978010 D.C.Watson, S.Leclerc, W.W.Wakarchuk, and N.M.Young (2011).
Enzymatic synthesis and properties of glycoconjugates with legionaminic acid as a replacement for neuraminic acid.
  Glycobiology, 21, 99.  
21036948 M.Kiyohara, K.Tanigawa, T.Chaiwangsri, T.Katayama, H.Ashida, and K.Yamamoto (2011).
An exo-{alpha}-sialidase from bifidobacteria involved in the degradation of sialyloligosaccharides in human milk and intestinal glycoconjugates.
  Glycobiology, 21, 437-447.  
21206954 Y.Li, H.Cao, H.Yu, Y.Chen, K.Lau, J.Qu, V.Thon, G.Sugiarto, and X.Chen (2011).
Identifying selective inhibitors against the human cytosolic sialidase NEU2 by substrate specificity studies.
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19797320 A.Bigi, L.Morosi, C.Pozzi, M.Forcella, G.Tettamanti, B.Venerando, E.Monti, and P.Fusi (2010).
Human sialidase NEU4 long and short are extrinsic proteins bound to outer mitochondrial membrane and the endoplasmic reticulum, respectively.
  Glycobiology, 20, 148-157.  
20124697 E.C.Schulz, P.Neumann, R.Gerardy-Schahn, G.M.Sheldrick, and R.Ficner (2010).
Structure analysis of endosialidase NF at 0.98 A resolution.
  Acta Crystallogr D Biol Crystallogr, 66, 176-180.
PDB code: 3ju4
20382985 G.L.Taylor (2010).
Introduction to phasing.
  Acta Crystallogr D Biol Crystallogr, 66, 325-338.  
19564377 D.Parker, G.Soong, P.Planet, J.Brower, A.J.Ratner, and A.Prince (2009).
The NanA neuraminidase of Streptococcus pneumoniae is involved in biofilm formation.
  Infect Immun, 77, 3722-3730.  
19594936 E.M.Quistgaard, and S.S.Thirup (2009).
Sequence and structural analysis of the Asp-box motif and Asp-box beta-propellers; a widespread propeller-type characteristic of the Vps10 domain family and several glycoside hydrolase families.
  BMC Struct Biol, 9, 46.  
18218621 S.L.Newstead, J.A.Potter, J.C.Wilson, G.Xu, C.H.Chien, A.G.Watts, S.G.Withers, and G.L.Taylor (2008).
The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates.
  J Biol Chem, 283, 9080-9088.
PDB codes: 2bf6 2vk5 2vk6 2vk7
18823396 T.Do, U.Henssge, S.C.Gilbert, D.Clark, and D.Beighton (2008).
Evidence for recombination between a sialidase (nanH) of Actinomyces naeslundii and Actinomyces oris, previously named 'Actinomyces naeslundii genospecies 1 and 2'.
  FEMS Microbiol Lett, 288, 156-162.  
16575518 E.Villar, and I.M.Barroso (2006).
Role of sialic acid-containing molecules in paramyxovirus entry into the host cell: a minireview.
  Glycoconj J, 23, 5.  
16352831 S.E.Haydel, and J.E.Clark-Curtiss (2006).
The Mycobacterium tuberculosis TrcR response regulator represses transcription of the intracellularly expressed Rv1057 gene, encoding a seven-bladed beta-propeller.
  J Bacteriol, 188, 150-159.  
15608653 K.Stummeyer, A.Dickmanns, M.Mühlenhoff, R.Gerardy-Schahn, and R.Ficner (2005).
Crystal structure of the polysialic acid-degrading endosialidase of bacteriophage K1F.
  Nat Struct Mol Biol, 12, 90-96.
PDB codes: 1v0e 1v0f
16332774 T.Sonke, S.Ernste, R.F.Tandler, B.Kaptein, W.P.Peeters, F.B.van Assema, M.G.Wubbolts, and H.E.Schoemaker (2005).
L-selective amidase with extremely broad substrate specificity from Ochrobactrum anthropi NCIMB 40321.
  Appl Environ Microbiol, 71, 7961-7973.  
14730352 C.P.Chiu, A.G.Watts, L.L.Lairson, M.Gilbert, D.Lim, W.W.Wakarchuk, S.G.Withers, and N.C.Strynadka (2004).
Structural analysis of the sialyltransferase CstII from Campylobacter jejuni in complex with a substrate analog.
  Nat Struct Mol Biol, 11, 163-170.
PDB codes: 1ro7 1ro8
15007099 E.R.Vimr, K.A.Kalivoda, E.L.Deszo, and S.M.Steenbergen (2004).
Diversity of microbial sialic acid metabolism.
  Microbiol Mol Biol Rev, 68, 132-153.  
15130470 M.F.Amaya, A.G.Watts, I.Damager, A.Wehenkel, T.Nguyen, A.Buschiazzo, G.Paris, A.C.Frasch, S.G.Withers, and P.M.Alzari (2004).
Structural insights into the catalytic mechanism of Trypanosoma cruzi trans-sialidase.
  Structure, 12, 775-784.
PDB codes: 1s0i 1s0j 1s0k 2ah2
15502328 S.Newstead, C.H.Chien, M.Taylor, and G.Taylor (2004).
Crystallization and atomic resolution X-ray diffraction of the catalytic domain of the large sialidase, nanI, from Clostridium perfringens.
  Acta Crystallogr D Biol Crystallogr, 60, 2063-2066.  
14695530 S.Pattison, M.Pankarican, C.A.Rupar, F.L.Graham, and S.A.Igdoura (2004).
Five novel mutations in the lysosomal sialidase gene (NEU1) in type II sialidosis patients and assessment of their impact on enzyme activity and intracellular targeting using adenovirus-mediated expression.
  Hum Mutat, 23, 32-39.  
15273299 S.Y.Reddy, and T.C.Bruice (2004).
Determination of enzyme mechanisms by molecular dynamics: studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase.
  Protein Sci, 13, 1965-1978.  
14747991 T.Pons, D.G.Naumoff, C.Martínez-Fleites, and L.Hernández (2004).
Three acidic residues are at the active site of a beta-propeller architecture in glycoside hydrolase families 32, 43, 62, and 68.
  Proteins, 54, 424-432.  
12974389 E.Tiralongo, I.Martensen, J.Grötzinger, J.Tiralongo, and R.Schauer (2003).
Trans-sialidase-like sequences from Trypanosoma congolense conserve most of the critical active site residues found in other trans-sialidases.
  Biol Chem, 384, 1203-1213.  
14573942 G.Taylor (2003).
The phase problem.
  Acta Crystallogr D Biol Crystallogr, 59, 1881-1890.  
14580216 J.N.Watson, V.Dookhun, T.J.Borgford, and A.J.Bennet (2003).
Mutagenesis of the conserved active-site tyrosine changes a retaining sialidase into an inverting sialidase.
  Biochemistry, 42, 12682-12690.  
14517945 V.Seyrantepe, H.Poupetova, R.Froissart, M.T.Zabot, I.Maire, and A.V.Pshezhetsky (2003).
Molecular pathology of NEU1 gene in sialidosis.
  Hum Mutat, 22, 343-352.  
11994155 D.R.Leggate, J.M.Bryant, M.B.Redpath, D.Head, P.W.Taylor, and J.P.Luzio (2002).
Expression, mutagenesis and kinetic analysis of recombinant K1E endosialidase to define the site of proteolytic processing and requirements for catalysis.
  Mol Microbiol, 44, 749-760.  
12071958 G.Montagna, M.L.Cremona, G.Paris, M.F.Amaya, A.Buschiazzo, P.M.Alzari, and A.C.Frasch (2002).
The trans-sialidase from the african trypanosome Trypanosoma brucei.
  Eur J Biochem, 269, 2941-2950.  
11799177 H.Connaris, T.Takimoto, R.Russell, S.Crennell, I.Moustafa, A.Portner, and G.Taylor (2002).
Probing the sialic acid binding site of the hemagglutinin-neuraminidase of Newcastle disease virus: identification of key amino acids involved in cell binding, catalysis, and fusion.
  J Virol, 76, 1816-1824.  
11937049 Z.Jawad, and M.Paoli (2002).
Novel sequences propel familiar folds.
  Structure, 10, 447-454.  
11746676 H.Kamei, K.Shimazaki, and Y.Nishi (2001).
Computational 3-D modeling and site-directed mutation of an antibody that binds Neu2en5Ac, a transition state analogue of a sialic acid.
  Proteins, 45, 285-296.  
11381099 M.J.Jedrzejas (2001).
Pneumococcal virulence factors: structure and function.
  Microbiol Mol Biol Rev, 65, 187.  
11308029 R.G.Kleineidam, S.Kruse, P.Roggentin, and R.Schauer (2001).
Elucidation of the role of functional amino acid residues of the small sialidase from Clostridium perfringens by site-directed mutagenesis.
  Biol Chem, 382, 313-319.  
11266614 R.R.Copley, R.B.Russell, and C.P.Ponting (2001).
Sialidase-like Asp-boxes: sequence-similar structures within different protein folds.
  Protein Sci, 10, 285-292.  
11298736 Y.Wang, K.Yamaguchi, Y.Shimada, X.Zhao, and T.Miyagi (2001).
Site-directed mutagenesis of human membrane-associated ganglioside sialidase: identification of amino-acid residues contributing to substrate specificity.
  Eur J Biochem, 268, 2201-2208.  
10619840 A.Buschiazzo, G.A.Tavares, O.Campetella, S.Spinelli, M.L.Cremona, G.París, M.F.Amaya, A.C.Frasch, and P.M.Alzari (2000).
Structural basis of sialyltransferase activity in trypanosomal sialidases.
  EMBO J, 19, 16-24.
PDB codes: 1mz5 1mz6
10801342 J.Yang, S.Schenkman, and B.A.Horenstein (2000).
Primary 13C and beta-secondary 2H KIEs for trans-sialidase. A snapshot of nucleophilic participation during catalysis.
  Biochemistry, 39, 5902-5910.  
11092845 S.Mizan, A.Henk, A.Stallings, M.Maier, and M.D.Lee (2000).
Cloning and characterization of sialidases with 2-6' and 2-3' sialyl lactose specificity from Pasteurella multocida.
  J Bacteriol, 182, 6874-6883.  
  9864307 R.Nádvorník, T.Vomastek, J.Janecek, Z.Techniková, and P.Branny (1999).
Pkg2, a novel transmembrane protein Ser/Thr kinase of Streptomyces granaticolor.
  J Bacteriol, 181, 15-23.  
10607670 V.Fülöp, and D.T.Jones (1999).
Beta propellers: structural rigidity and functional diversity.
  Curr Opin Struct Biol, 9, 715-721.  
9753433 K.Gruber, G.Klintschar, M.Hayn, A.Schlacher, W.Steiner, and C.Kratky (1998).
Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies.
  Biochemistry, 37, 13475-13485.
PDB code: 1yna
9626695 T.Pons, G.Chinea, O.Olmea, A.Beldarraín, H.Roca, G.Padrón, and A.Valencia (1998).
Structural model of Dex protein from Penicillium minioluteum and its implications in the mechanism of catalysis.
  Proteins, 31, 345-354.  
9829697 T.Pons, O.Olmea, G.Chinea, A.Beldarraín, G.Márquez, N.Acosta, L.Rodríguez, and A.Valencia (1998).
Structural model for family 32 of glycosyl-hydrolase enzymes.
  Proteins, 33, 383-395.  
9562562 Y.Luo, S.C.Li, M.Y.Chou, Y.T.Li, and M.Luo (1998).
The crystal structure of an intramolecular trans-sialidase with a NeuAc alpha2-->3Gal specificity.
  Structure, 6, 521-530.
PDB codes: 1sli 1sll
9054950 A.V.Pshezhetsky, C.Richard, L.Michaud, S.Igdoura, S.Wang, M.A.Elsliger, J.Qu, D.Leclerc, R.Gravel, L.Dallaire, and M.Potier (1997).
Cloning, expression and chromosomal mapping of human lysosomal sialidase and characterization of mutations in sialidosis.
  Nat Genet, 15, 316-320.  
  9223510 J.P.Langedijk, F.J.Daus, and J.T.van Oirschot (1997).
Sequence and structure alignment of Paramyxoviridae attachment proteins and discovery of enzymatic activity for a morbillivirus hemagglutinin.
  J Virol, 71, 6155-6167.  
  9094607 L.V.Gubareva, M.J.Robinson, R.C.Bethell, and R.G.Webster (1997).
Catalytic and framework mutations in the neuraminidase active site of influenza viruses that are resistant to 4-guanidino-Neu5Ac2en.
  J Virol, 71, 3385-3390.  
8990162 T.A.Springer (1997).
Folding of the N-terminal, ligand-binding region of integrin alpha-subunits into a beta-propeller domain.
  Proc Natl Acad Sci U S A, 94, 65-72.  
9365983 V.C.Epa (1997).
Modeling the paramyxovirus hemagglutinin-neuraminidase protein.
  Proteins, 29, 264-281.  
8994884 G.Taylor (1996).
Sialidases: structures, biological significance and therapeutic potential.
  Curr Opin Struct Biol, 6, 830-837.  
8981083 J.C.Wilson, D.C.Kong, Y.T.Li, and M.von Itzstein (1996).
A 1H NMR investigation of the hydrolysis of a synthetic substrate by KDN-sialidase from Crassostrea virginica.
  Glycoconj J, 13, 927-931.  
  8896448 L.Eichinger, L.Bomblies, J.Vandekerckhove, M.Schleicher, and J.Gettemans (1996).
A novel type of protein kinase phosphorylates actin in the actin-fragmin complex.
  EMBO J, 15, 5547-5556.  
8913694 M.von Itzstein, and P.Colman (1996).
Design and synthesis of carbohydrate-based inhibitors of protein-carbohydrate interactions.
  Curr Opin Struct Biol, 6, 703-709.  
8591030 A.Gaskell, S.Crennell, and G.Taylor (1995).
The three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll.
  Structure, 3, 1197-1205.
PDB codes: 1eur 1eus 1eut 1euu
8535779 G.Davies, and B.Henrissat (1995).
Structures and mechanisms of glycosyl hydrolases.
  Structure, 3, 853-859.  
  7603411 K.E.Sanderson, A.Hessel, and K.E.Rudd (1995).
Genetic map of Salmonella typhimurium, edition VIII.
  Microbiol Rev, 59, 241-303.  
7735834 M.Ghosh, C.Anthony, K.Harlos, M.G.Goodwin, and C.Blake (1995).
The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 A.
  Structure, 3, 177-187.
PDB code: 1h4i
7822422 M.Way, M.Sanders, C.Garcia, J.Sakai, and P.Matsudaira (1995).
Sequence and domain organization of scruin, an actin-cross-linking protein in the acrosomal process of Limulus sperm.
  J Cell Biol, 128, 51-60.  
8749373 V.S.Lamzin, Z.Dauter, and K.S.Wilson (1995).
How nature deals with stereoisomers.
  Curr Opin Struct Biol, 5, 830-836.  
7881905 G.E.Norris, T.J.Stillman, B.F.Anderson, and E.N.Baker (1994).
The three-dimensional structure of PNGase F, a glycosylasparaginase from Flavobacterium meningosepticum.
  Structure, 2, 1049-1059.
PDB code: 1pgs
7937731 L.Holm, and C.Sander (1994).
Searching protein structure databases has come of age.
  Proteins, 19, 165-173.  
  8063384 M.Cámara, G.J.Boulnois, P.W.Andrew, and T.J.Mitchell (1994).
A neuraminidase from Streptococcus pneumoniae has the features of a surface protein.
  Infect Immun, 62, 3688-3695.  
  7849585 P.M.Colman (1994).
Influenza virus neuraminidase: structure, antibodies, and inhibitors.
  Protein Sci, 3, 1687-1696.  
7922030 S.Crennell, E.Garman, G.Laver, E.Vimr, and G.Taylor (1994).
Crystal structure of Vibrio cholerae neuraminidase reveals dual lectin-like domains in addition to the catalytic domain.
  Structure, 2, 535-544.
PDB code: 1kit
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.